[English] 日本語
Yorodumi
- PDB-3uyu: Structural basis for the antifreeze activity of an ice-binding pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uyu
TitleStructural basis for the antifreeze activity of an ice-binding protein (LeIBP) from Arctic yeast
ComponentsAntifreeze protein
KeywordsANTIFREEZE PROTEIN / right-handed beta-helix fold / ICE BINDING PROTEIN
Function / homologyice binding / Ice-binding protein / Ice-binding-like / extracellular region / Ice-binding protein
Function and homology information
Biological speciesLeucosporidium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsLee, J.H. / Park, A.K. / Do, H. / Park, K.S. / Moh, S.H. / Chi, Y.M. / Kim, H.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for the antifreeze activity of an ice-binding protein from an Arctic yeast.
Authors: Lee, J.H. / Park, A.K. / Do, H. / Park, K.S. / Moh, S.H. / Chi, Y.M. / Kim, H.J.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antifreeze protein
B: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3214
Polymers50,1372
Non-polymers1842
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-19 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.580, 97.580, 106.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Antifreeze protein


Mass: 25068.494 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-261 / Mutation: L86M, L172M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leucosporidium (fungus) / Strain: AY30 / Gene: AFP / Production host: Escherichia coli (E. coli) / References: UniProt: C7F6X3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate, pH 4.5, 1.2M ammonium sulfate, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98227 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 29, 2011
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98227 Å / Relative weight: 1
ReflectionResolution: 1.57→36 Å / Num. all: 71952 / Num. obs: 71520 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.57→1.66 Å / % possible all: 98.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.57→31.59 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 1.461 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25073 3614 5.1 %RANDOM
Rwork0.21597 ---
all0.21824 71520 --
obs0.21774 67692 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.605 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.57→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 12 458 3811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223416
X-RAY DIFFRACTIONr_angle_refined_deg2.2571.9554671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1525.606132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64515474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.981158
X-RAY DIFFRACTIONr_chiral_restr0.3080.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212602
X-RAY DIFFRACTIONr_mcbond_it1.271.52275
X-RAY DIFFRACTIONr_mcangle_it2.07123638
X-RAY DIFFRACTIONr_scbond_it3.70131141
X-RAY DIFFRACTIONr_scangle_it5.2964.51033
LS refinement shellResolution: 1.574→1.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 244 -
Rwork0.245 4926 -
obs--99.38 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more